From: Viswanath Pasumarthi (
Date: Tue Feb 17 2015 - 05:12:56 CST


Since the NAMDEnergy plugin doesn't support evaluation of bonding energies
between two atom selections, is there any other third-party plugin/code
available to do the job? Bonding energy plot obtained from NAMD Plot shows
abnormal behavior in my system and I would like to debug by analyzing
individual bonding interactions.

And when bond energies are calculated with a single atom selection, does
the plugin
calculate all the bonding energies that selection is involved in? For
example, if atom selection is "type OW" in water, it will give total
bonding energies the OW atom type involves in, as a function of frame. Is
that correct?